Package htsjdk.samtools

Examples of htsjdk.samtools.SAMRecordQueryNameComparator

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            return mergingIterator;
        }


        final SortingCollection<SAMRecord> alignmentSorter = SortingCollection.newInstance(SAMRecord.class,
                    new BAMRecordCodec(header), new SAMRecordQueryNameComparator(), MAX_RECORDS_IN_RAM);

        int count = 0;
        while (mergingIterator.hasNext()) {
            alignmentSorter.add(mergingIterator.next());
            count++;
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        ////////////////////////////////////////////////////////////////////////////
        // Build a sorting collection to use if we are sanitizing
        ////////////////////////////////////////////////////////////////////////////
        final SortingCollection<SAMRecord> sorter;
        if (sanitizing) {
            sorter = SortingCollection.newInstance(SAMRecord.class, new BAMRecordCodec(outHeader), new SAMRecordQueryNameComparator(), MAX_RECORDS_IN_RAM);
        }
        else {
            sorter = null;
        }
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        SAMFileWriterFactory.setDefaultCreateMd5File(CREATE_MD5_FILE);
        final SAMFileWriter out = new SAMFileWriterFactory().makeSAMOrBAMWriter(outHeader, false, OUTPUT);

        // Iterate over the records, revert original base qualities, and push them into a SortingCollection by queryname
        final SortingCollection<SAMRecord> sorter = SortingCollection.newInstance(SAMRecord.class, new BAMRecordCodec(outHeader),
                new SAMRecordQueryNameComparator(), MAX_RECORDS_IN_RAM);
        final ProgressLogger revertingProgress = new ProgressLogger(log, 1000000, " reverted OQs");
        int numOriginalQualitiesRestored = 0;
        for (final SAMRecord record : in) {
            // Clean up reads that map off the end of the reference
            AbstractAlignmentMerger.createNewCigarsIfMapsOffEndOfReference(record);
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            }
            else {
                log.info("Sorting input into queryname order.");
                final SortingCollection<SAMRecord> sorter = SortingCollection.newInstance(SAMRecord.class,
                                                                                          new BAMRecordCodec(header),
                                                                                          new SAMRecordQueryNameComparator(),
                                                                                          MAX_RECORDS_IN_RAM,
                                                                                          TMP_DIR);
                while (tmp.hasNext()) {
                    sorter.add(tmp.next());
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Related Classes of htsjdk.samtools.SAMRecordQueryNameComparator

  • picard.sam.FixMateInformation
  • picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
  • picard.sam.RevertSam
  • picard.sam.SamAlignmentMerger
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